BMC Bioinformatics

Table 1 Sequence-sequence comparison F-measure for clustered sequences

From: Evaluation and improvements of clustering algorithms for detecting remote homologous protein families

Family
	TransClust				HiFix				MCL				SCPS
Dataset	F-measure	Clusters	Precision	Recall	F-measure	Clusters	Precision	Recall	F-measure	Clusters	Precision	Recall	F-measure	Clusters	Precision	Recall
A-10	0.494	1757	0.834	0.409	0.467	2780	0.463	0.692	0.352	2310	0.923	0.389	-
A-20	0.573	2013	0.885	0.494	0.491	3270	0.556	0.732	0.398	4125	0.999	0.278	-
A-30	0.675	2561	0.912	0.628	0.583	3749	0.561	0.885	0.415	1827	0.351	0.773	-
A-50	0.721	3221	0.903	0.709	0.608	4861	0.562	0.945	0.457	1912	0.702	0.445	-
A-70	0.739	3486	0.904	0.733	0.630	4921	0.616	0.873	0.474	2323	0.752	0.482	-
A-90	0.758	3630	0.913	0.753	0.653	4973	0.625	0.895	0.511	2824	0.815	0.512	-
A-95	0.766	3715	0.916	0.765	0.654	4992	0.629	0.907	0.527	2873	0.527	0.813	-
GOLD	0.914	96	0.905	0.968	0.902	99	0.960	0.895	0.880	56	0.808	0.942	-
Super-family
A-10	0.377	1757	0.917	0.281	0.337	2780	0.993	0.274	0.270	3270	0.997	0.180	0.297	658	0.387	0.221
A-20	0.450	2013	0.954	0.347	0.362	3270	0.993	0.293	0.282	4024	0.999	0.191	0.352	701	0.400	0.323
A-30	0.551	2561	0.551	0.440	0.473	3749	0.994	0.414	0.333	3745	0.998	0.235	0.473	792	0.494	0.364
A-50	0.609	3221	0.995	0.499	0.507	4861	0.992	0.457	0.351	3048	0.847	0.310	0.557	753	0.618	0.546
A-70	0.631	3486	0.997	0.519	0.539	4921	0.990	0.495	0.377	2086	0.875	0.335	0.581	493	0.649	0.518
A-90	0.654	3630	0.996	0.544	0.560	4973	0.989	0.528	0.426	2549	0.922	0.364	0.607	633	0.680	0.531
A-95	0.659	3715	0.996	0.552	0.563	4986	0.990	0.542	0.435	2616	0.912	0.378	0.615	940	0.686	0.542
GOLD	0.865	23	1	0.765	0.915	13	0.998	0.852	0.827	24	1	0.712	0.904	4	0.864	0.983

Number of clusters found, and weighted mean precision and recall values for each clustering algorithm are shown. Best values are shown in bold.

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